chr4-78865702-GGT-TCC

Variant names:

• chr4-78865702-GGT-TCC
• NM_198892.2:c.1213_1215delGGTinsTCC
• BMP2K p.Gly405Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_198892.2(BMP2K):​c.1213_1215delGGTinsTCC​(p.Gly405Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G405R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMP2K NM_198892.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 0 publications found

Genes affected

BMP2K (HGNC:18041): (BMP2 inducible kinase) This gene is the human homolog of mouse BMP-2-inducible kinase. Bone morphogenic proteins (BMPs) play a key role in skeletal development and patterning. Expression of the mouse gene is increased during BMP-2 induced differentiation and the gene product is a putative serine/threonine protein kinase containing a nuclear localization signal. Therefore, the protein encoded by this human homolog is thought to be a protein kinase with a putative regulatory role in attenuating the program of osteoblast differentiation. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198892.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMP2K	NM_198892.2	MANE Select	c.1213_1215delGGTinsTCC	p.Gly405Ser	missense	N/A	NP_942595.1	Q9NSY1-1
	BMP2K	NM_001419799.1		c.1213_1215delGGTinsTCC	p.Gly405Ser	missense	N/A	NP_001406728.1
	BMP2K	NM_001419800.1		c.1213_1215delGGTinsTCC	p.Gly405Ser	missense	N/A	NP_001406729.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMP2K	ENST00000502613.3	TSL:1 MANE Select	c.1213_1215delGGTinsTCC	p.Gly405Ser	missense	N/A	ENSP00000424668.2	Q9NSY1-1
	BMP2K	ENST00000502871.5	TSL:1	c.1213_1215delGGTinsTCC	p.Gly405Ser	missense	N/A	ENSP00000421768.1	Q9NSY1-2
	BMP2K	ENST00000389010.7	TSL:1	n.*189_*191delGGTinsTCC		non_coding_transcript_exon	Exon 11 of 15	ENSP00000373662.3	K4DI97

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr4-79786856;